From bb50c7e5050d35b57660f47374976d83318dcd87 Mon Sep 17 00:00:00 2001
From: Norbert Podhorszki <pnorbert@ornl.gov>
Date: Mon, 3 Apr 2017 11:17:42 -0400
Subject: [PATCH] Fixes to ADIOS1 Reader class just to make it compile.
---
.../hello/adios1Writer/helloADIOS1Writer.cpp | 2 +
.../adios1Writer/helloADIOS1Writer_nompi.cpp | 2 +-
include/engine/adios1/ADIOS1Reader.h | 35 +++--
source/engine/adios1/ADIOS1Reader.cpp | 132 ++++++------------
4 files changed, 58 insertions(+), 113 deletions(-)
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer.cpp b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
index 9543ec43b..dcfc43457 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
@@ -11,7 +11,9 @@
#include <iostream>
#include <vector>
+#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
+#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
index eb282251d..f68529812 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
@@ -16,7 +16,7 @@
int main(int argc, char *argv[])
{
const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
+ adios::ADIOS adios( adios::Verbose::INFO,adiosDebug );
// Application variable
std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
diff --git a/include/engine/adios1/ADIOS1Reader.h b/include/engine/adios1/ADIOS1Reader.h
index 70b89700a..1f92a1078 100644
--- a/include/engine/adios1/ADIOS1Reader.h
+++ b/include/engine/adios1/ADIOS1Reader.h
@@ -10,8 +10,8 @@
* Author: pnb
*/
-#ifndef BPFILEREADER_H_
-#define BPFILEREADER_H_
+#ifndef ADIOS1READER_H_
+#define ADIOS1READER_H_
#include <iostream> //this must go away
@@ -23,7 +23,13 @@
namespace adios
{
-class BPFileReader : public Engine
+#ifdef ADIOS_NOMPI
+#define _NOMPI 1
+#endif
+#include "adios_read_v2.h" // this is adios 1.x header file
+
+
+class ADIOS1Reader : public Engine
{
public:
@@ -37,13 +43,13 @@ public:
* @param debugMode
* @param hostLanguage
*/
- BPFileReader(ADIOS &adios, const std::string name,
+ ADIOS1Reader(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method, const IOMode iomode,
const float timeout_sec, const bool debugMode = false,
const unsigned int nthreads = 1);
- ~BPFileReader();
+ ~ADIOS1Reader();
Variable<void> *InquireVariable(const std::string name,
const bool readIn = true);
@@ -92,24 +98,13 @@ public:
void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- // format::BP1Writer m_BP1Writer; ///< format object will provide the required
- // BP functionality to be applied on m_Buffer and m_Transports
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
+ void Init(); ///< called from constructor, gets the selected ADIOS1 transport method from settings
template <class T>
Variable<T> *InquireVariableCommon(const std::string name, const bool readIn)
{
- std::cout << "Hello BPReaderCommon\n";
+ std::cout << "Hello ADIOS1Reader::InquireVariableCommon\n";
// here read variable metadata (dimensions, type, etc.)...then create a
// Variable like below:
@@ -117,8 +112,10 @@ private:
// return &variable; //return address if success
return nullptr; // on failure
}
+
+ enum ADIOS_READ_METHOD read_method = ADIOS_READ_METHOD_BP;
};
} // end namespace adios
-#endif /* BPFILEREADER_H_ */
+#endif /* ADIOS1READER_H_ */
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index 406c752d3..5472099fc 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -2,222 +2,168 @@
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
- * BPFileReader.cpp
+ * ADIOS1Reader.cpp
*
* Created on: Feb 27, 2017
* Author: wfg
*/
-#include "engine/bp/BPFileReader.h"
+#include "engine/adios1/ADIOS1Reader.h"
+#include "ADIOS.h"
-#include "core/Support.h"
-#include "functions/adiosFunctions.h" //CSVToVector
-#include "transport/file/FileDescriptor.h" // uses POSIX
-#include "transport/file/FilePointer.h" // uses C FILE*
-
-// supported transports
-#include "transport/file/FStream.h" // uses C++ fstream
+extern int adios_verbose_level;
+extern int adios_errno;
namespace adios
{
-BPFileReader::BPFileReader(ADIOS &adios, const std::string name,
+ADIOS1Reader::ADIOS1Reader(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method, const IOMode iomode,
const float timeout_sec, const bool debugMode,
const unsigned int nthreads)
-: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method, debugMode,
- nthreads, " BPFileReader constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+: Engine(adios, "ADIOS1Reader", name, accessMode, mpiComm, method,
+ debugMode, nthreads,
+ " ADIOS1Reader constructor (or call to ADIOS Open).\n")
{
Init();
+ adios_read_init_method(read_method, m_MPIComm, "");
}
-BPFileReader::~BPFileReader() {}
+ADIOS1Reader::~ADIOS1Reader()
+{
+ adios_read_finalize_method(read_method);
+}
Variable<void> *
-BPFileReader::InquireVariable(const std::string name,
+ADIOS1Reader::InquireVariable(const std::string name,
const bool readIn) // not yet implemented
{
return nullptr;
}
-Variable<char> *BPFileReader::InquireVariableChar(const std::string name,
+Variable<char> *ADIOS1Reader::InquireVariableChar(const std::string name,
const bool readIn)
{
return InquireVariableCommon<char>(name, readIn);
}
Variable<unsigned char> *
-BPFileReader::InquireVariableUChar(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableUChar(const std::string name, const bool readIn)
{
return InquireVariableCommon<unsigned char>(name, readIn);
}
-Variable<short> *BPFileReader::InquireVariableShort(const std::string name,
+Variable<short> *ADIOS1Reader::InquireVariableShort(const std::string name,
const bool readIn)
{
return InquireVariableCommon<short>(name, readIn);
}
Variable<unsigned short> *
-BPFileReader::InquireVariableUShort(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableUShort(const std::string name, const bool readIn)
{
return InquireVariableCommon<unsigned short>(name, readIn);
}
-Variable<int> *BPFileReader::InquireVariableInt(const std::string name,
+Variable<int> *ADIOS1Reader::InquireVariableInt(const std::string name,
const bool readIn)
{
return InquireVariableCommon<int>(name, readIn);
}
Variable<unsigned int> *
-BPFileReader::InquireVariableUInt(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableUInt(const std::string name, const bool readIn)
{
return InquireVariableCommon<unsigned int>(name, readIn);
}
-Variable<long int> *BPFileReader::InquireVariableLInt(const std::string name,
+Variable<long int> *ADIOS1Reader::InquireVariableLInt(const std::string name,
const bool readIn)
{
return InquireVariableCommon<long int>(name, readIn);
}
Variable<unsigned long int> *
-BPFileReader::InquireVariableULInt(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableULInt(const std::string name, const bool readIn)
{
return InquireVariableCommon<unsigned long int>(name, readIn);
}
Variable<long long int> *
-BPFileReader::InquireVariableLLInt(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableLLInt(const std::string name, const bool readIn)
{
return InquireVariableCommon<long long int>(name, readIn);
}
Variable<unsigned long long int> *
-BPFileReader::InquireVariableULLInt(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableULLInt(const std::string name, const bool readIn)
{
return InquireVariableCommon<unsigned long long int>(name, readIn);
}
-Variable<float> *BPFileReader::InquireVariableFloat(const std::string name,
+Variable<float> *ADIOS1Reader::InquireVariableFloat(const std::string name,
const bool readIn)
{
return InquireVariableCommon<float>(name, readIn);
}
-Variable<double> *BPFileReader::InquireVariableDouble(const std::string name,
+Variable<double> *ADIOS1Reader::InquireVariableDouble(const std::string name,
const bool readIn)
{
return InquireVariableCommon<double>(name, readIn);
}
Variable<long double> *
-BPFileReader::InquireVariableLDouble(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableLDouble(const std::string name, const bool readIn)
{
return InquireVariableCommon<long double>(name, readIn);
}
Variable<std::complex<float>> *
-BPFileReader::InquireVariableCFloat(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableCFloat(const std::string name, const bool readIn)
{
return InquireVariableCommon<std::complex<float>>(name, readIn);
}
Variable<std::complex<double>> *
-BPFileReader::InquireVariableCDouble(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableCDouble(const std::string name, const bool readIn)
{
return InquireVariableCommon<std::complex<double>>(name, readIn);
}
Variable<std::complex<long double>> *
-BPFileReader::InquireVariableCLDouble(const std::string name, const bool readIn)
+ADIOS1Reader::InquireVariableCLDouble(const std::string name, const bool readIn)
{
return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
-VariableCompound *BPFileReader::InquireVariableCompound(const std::string name,
+VariableCompound *ADIOS1Reader::InquireVariableCompound(const std::string name,
const bool readIn)
{
return nullptr;
}
-void BPFileReader::Close(const int transportIndex) {}
+void ADIOS1Reader::Close(const int transportIndex) {}
// PRIVATE
-void BPFileReader::Init()
+void ADIOS1Reader::Init()
{
if (m_DebugMode == true)
{
if (m_AccessMode != "r" && m_AccessMode != "read")
throw std::invalid_argument(
- "ERROR: BPFileReader doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or BPFileReader constructor\n");
- }
-
- InitCapsules();
- InitTransports();
-}
-
-void BPFileReader::InitCapsules()
-{
- // here init memory capsules
-}
-
-void BPFileReader::InitTransports() // maybe move this?
-{
- if (m_DebugMode == true)
- {
- if (TransportNamesUniqueness() == false)
- {
- throw std::invalid_argument(
- "ERROR: two transports of the same kind (e.g file IO) "
- "can't have the same name, modify with name= in Method "
- "AddTransport\n");
- }
+ "ERROR: ADIOS1Reader doesn't support access mode " + m_AccessMode +
+ ", in call to ADIOS Open or ADIOS1Reader constructor\n");
}
for (const auto ¶meters : m_Method.m_TransportParameters)
{
auto itTransport = parameters.find("transport");
- if (itTransport->second == "file" || itTransport->second == "File")
+ if (itTransport->second == "file" || itTransport->second == "File" ||
+ itTransport->second == "bp" || itTransport->second == "BP")
{
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- auto file =
- std::make_shared<transport::FileDescriptor>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "FILE*" || itLibrary->second == "stdio.h")
- {
- auto file =
- std::make_shared<transport::FilePointer>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "fstream" ||
- itLibrary->second == "std::fstream")
- {
- auto file =
- std::make_shared<transport::FStream>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "MPI-IO")
- {
- }
- else
- {
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
- }
+ read_method = ADIOS_READ_METHOD_BP;
}
else
{
--
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